Protein Data Bank
Protein Data Bank is a great source for information about proteins. In addition to performing BLAST
matches, it also provides links to published literature and allows the user to view the structure of the
protein. It offers many ways to search for matches. The most useful when annotating is by search by
sequence.
This is the front page of the PDB website. To search, click on the search tab in the upper left hand
corner.
PDB gives many search options. If we’re just beginning to investigate a protein, it’s best to start with
“sequence”.
This page accepts protein sequences with either the 1- or 3-letter amino acid abbreviations. Don’t post
the nucleotide sequence, as it is not accepted. Select the “Use sequence” radio button, post your
sequence, and hit search. When the results page comes up, you will see multiple results. As an example,
the first result from the search above is below.
There’s a lot of information given with each result, so we’ll sort though it line by line. The combination
of letters and numbers in the left hand corner is the PDB ID. You can search using this ID later to find the
proteins of this category. The two icons furthest to the left in the corner (the blue arrow and list) allow
you to download or view, respectively, a printout of the protein match. This printout gives a great deal
of useful information in a text-only format that facilitates copying and pasting. The eye icon gives you a
chance to look at the jmol structure of the protein match. The question mark leads to a help page.
The purple link at the top of the page leads to the PDB structural report for this protein.
One feature of the main results page is the color-coded BLAST results. Above the results is the numerical
BLAST output. Length is the number of amino acids in the alignment sequence. The score is calculated
based on the number of identities, in which the amino acid is the same for both sequences, positives,
where a positive value is generated by the algorithm and mismatches, where a negative value is
generated. The E-value is also given; the lower the E-value, the better the alignment of the two proteins.
Gaps indicate regions in which one protein contains amino acid sequences not found in the other
protein. PDB color-codes the results by these criteria. Identities are marked black, with the amino acid
abbreviation repeated in the row between the two sequences. Positives are marked yellow, with a +
between the sequences. Non-matching amino acids are marked in red.
The amino acids marked grey and blue are slightly more confusing. They indicate amino acids that are
present in one protein sequence but not the other (gaps).
Once you’ve looked at the BLAST results, clicking on the grey text to bring up the structural report is a
good next step. Once you do that, you will see a page with many blue links. Each blue link can be clicked
to go to a different page. For example, you could click on hydrolase activity under molecular function to
search for all proteins that display hydrolase activity.
This page gives a great deal of data about the protein. In addition, it also supplies many useful tools. On
the right hand side of the page, you see a colorful protein with links under it. Clicking on each of those
links will allow you to open the protein in a different rendering agent. Each rendering agent allows you
to rotate the protein and zoom in and out. There are also different viewing modes you can take
advantage of, such as space fill and ribbon.
Another useful link is the EC number, which is a classification number that is determined by what type of
reaction an enzyme catalyzes. Although the names of two proteins may be different, if the EC number is
the same, the proteins have the same function.
The link to the PubMed abstract is also very useful. When clicked, this link opens the abstract of the
paper that contains the information about this protein.
In addition to the abstract, the paper lists keywords that pertain to this protein. By typing one or more
of those keywords into the search box, you can search for other proteins whose abstracts list those
keywords, such as carboxylic ester hydrolases.
If you need to find the protein again, simply write down the PDB ID. Then, when you’re ready to look at
the protein again, simply type the ID number into the search box at the top of the page.
We are then directed back to the structural report for the protein.
Another useful feature of PDB is that, for the duration of your session, it keeps your queries and search
results in memory. They can be easily accessed from the upper left corner of the page.
You may want to place your results in a spreadsheet. In this case, PDB gives you the opportunity to
export the information you want in Excel format. To do this, go to the toolbar on the left, click on
Tabulate, and then on Custom Report.
The picture below represents some of the options available for data that can be included in the Excel
report. Simply click as few or as many as you would like, then scroll down and click create report. For
this example, I’ve highlighted Sequence and Keywords. Notice that selecting the bolded category on the
left hand side of the page selects all of the information directly to the right of that heading.
Once we click create report, we are taken to a page that shows the attributes we selected. Simply click
on the green Excel logo in the upper right corner to download the Excel file. The report can also be
downloaded as a CSV file.